1) The changes seem to be designed to help shoddy Linux ports--e.g. those that haven't been updated in awhile or that have very poor performance. I worry that developers will see this as an alternative to native Linux ports, and instead of getting awesome games that work on Linux without WINE (see: Beamdog's awesome Enhanced Editions of classic Interplay/Bioware/Black Isle RPGs), we'll simply see all Linux games running in WINE containers. WINE is great, but it's not perfect. When Proton was first enabled, I tried running System Shock Enhanced Edition and it crashes immediately. System Shock Classic, on the other hand, is certified for OSX and Linux and runs properly (although for all I know SSC might just be a tweaked WINE container).
2) Not all games work with WINE. That's why there's the WINE compatibility list, along with community forums dedicated to making tweaks to get the games running. I fear that throwing everything at WINE effectively puts the onus of getting the game working onto the WINE community, rather than the game's developers. I suppose in Best Case scenario (after native Linux builds, of course), game developers could contract out the CrossWeavers guys to help get their specific game working within WINE and that might still be cheaper than the resources required to build the game natively. But whether they'll actually do that remains to be seen.